Not just the CIA — Secret Service, FBI, DoD, DHS, etc — all work with mainstream media; same is true for any large domestic media company in any country working with local governments, including: China, Russia, etc.
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Source:
How the Central Intelligence Agency works with Hollywood
I think they’re negative only depending on your personal politics. They’re never depicted as incompetent, technologically challenged, or overly beaurocratic.
I don't think so. You are right that they aren't depicted as incompetent, technologically challenged, or overly bureaucratic. But they are also depicted as terrorists sponsoring, war mongering, torturous murderers that show little regard for life. I would say those are widely accepted as bad traits and not just my personal politics.